diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index 4e23d4d62..e1c415183 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -87,7 +87,9 @@ public class VariantsToTable extends RodWalker { } }); getters.put("QUAL", new Getter() { public String get(VariantContext vc) { return Double.toString(vc.getPhredScaledQual()); } }); - getters.put("FILTER", new Getter() { public String get(VariantContext vc) { return Utils.join(",", vc.getFilters()); } }); + getters.put("FILTER", new Getter() { public String get(VariantContext vc) { + return vc.isNotFiltered() ? "PASS" : Utils.join(",", vc.getFilters()); } + }); getters.put("HET", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount()); } }); getters.put("HOM-REF", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomRefCount()); } });